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Babelomics 5.0: functional interpretation for new generations of genomic data

Roberto Alonso, Francisco Salavert, Francisco Garcia-Garcia, Jose Carbonell-Caballero, Marta Bleda, Luz Garcia-Alonso, Alba Sanchis-Juan, Daniel Perez-Gil, Pablo Marin-Garcia, Ruben Sanchez, Cankut Cubuk, Marta R. Hidalgo (+7 others)
2015 Nucleic Acids Research  
Babelomics has been running for more than one decade offering a user-friendly interface for the functional analysis of gene expression and genomic data.  ...  analysis algorithms for the interpretation of the results of such tests in the proper functional context.  ...  ACKNOWLEDGEMENTS Part of this work has been carried out in the context of the HPC4G initiative (http://www.hpc4g.org) and the Bull-CIPF Chair for Computational Genomics.  ... 
doi:10.1093/nar/gkv384 pmid:25897133 pmcid:PMC4489263 fatcat:q7yzzd2eyneefotrrxnsl2ho7u

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

Jing Wang, Suhas Vasaikar, Zhiao Shi, Michael Greer, Bing Zhang
2017 Nucleic Acids Research  
Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data.  ...  of high-throughput omics data.  ...  2016 (17) and Babelomics 5.0 (18), focusing on the new features introduced in WebGestalt 2017.  ... 
doi:10.1093/nar/gkx356 pmid:28472511 pmcid:PMC5570149 fatcat:5pvkxtiq55e7jdbckg6asphszm

DNA Repair and Immune Response Pathways Are Deregulated in Melanocyte-Keratinocyte Co-cultures Derived From the Healthy Skin of Familial Melanoma Patients

Miriam Potrony, Tariq Sami Haddad, Gemma Tell-Martí, Pol Gimenez-Xavier, Carlos Leon, Marta Pevida, Judit Mateu, Celia Badenas, Cristina Carrera, Josep Malvehy, Paula Aguilera, Sara Llames (+4 others)
2021 Frontiers in Medicine  
Functional enrichment analysis of this profile showed a downregulation of pathways related to DNA repair and immune response in familial melanoma (P < 0.05).  ...  Familial melanoma accounts for 10% of cases, being CDKN2A the main high-risk gene. However, the mechanisms underlying melanomagenesis in these cases remain poorly understood.  ...  We used commercial qPCR assays (IDT, Coralville, IA, US) and the TaqMan Data Analysis Whole transcriptome expression data analysis was carried out using the free tool Babelomics 5.0 (12).  ... 
doi:10.3389/fmed.2021.692341 pmid:34660619 pmcid:PMC8517393 fatcat:e7szp26l75ft3g4rubs6xh647e

Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis

Dafne Pérez-Montarelo, Ole Madsen, Estefânia Alves, M. Carmen Rodríguez, Josep María Folch, José Luis Noguera, Martien A. M. Groenen, Ana I. Fernández
2014 Physiological Genomics  
Functional analyses supported the key role of the hypothalamus in the regulation of growth, fat accumulation, and energy expenditure. Moreover, 58,927 potentially new isoforms were detected.  ...  This study allows us to propose strong candidate genes for growth and fatness based on expression patterns, genomic location, and network interactions.  ...  ., and A.I.F. analyzed data; D.P.-M., O.M., and A.I.F. interpreted results of experiments; D.P.-M. prepared figures; D.P.-M. and A.I.F. drafted manuscript; D.P.  ... 
doi:10.1152/physiolgenomics.00151.2013 pmid:24280257 pmcid:PMC3949103 fatcat:mls7bncd4bab3ioc7w4qchs5qa

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

Ángel M. Martínez-Montes, Almudena Fernández, María Muñoz, Jose Luis Noguera, Josep M. Folch, Ana I. Fernández, Roberta Davoli
2018 PLoS ONE  
The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic  ...  from RNA-Seq data.  ...  We want to thanks Fabián Garcia and Anna Mercadé for technical assistance. The animal material was generated under the CPE03-010-C3 INIA grant.  ... 
doi:10.1371/journal.pone.0190184 pmid:29522525 pmcid:PMC5844516 fatcat:a7k5rup7cvgtlfrihuxfi3o5sy

Charting the NF-κB Pathway Interactome Map

Paolo Tieri, Alberto Termanini, Elena Bellavista, Stefano Salvioli, Miriam Capri, Claudio Franceschi, Karen L. Mossman
2012 PLoS ONE  
Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct  ...  This interactome is intended as an open network resource available for further development, refinement and analysis.  ...  The Babelomics suite for functional analysis identified 16 duplicates leading to a valid list of 410 IDs.  ... 
doi:10.1371/journal.pone.0032678 pmid:22403694 pmcid:PMC3293857 fatcat:omhalpmlhzaxrji3l5kpyfzkae

Charting the NF-kB pathway interactome map

Paolo Tieri, Paolo Tieri, Alberto Termanini, Elena Bellavista, Stefano Salvioli, Claudio Franceschi
2010 Nature Precedings  
Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct  ...  This interactome is intended as an open network resource available for further development, refinement and analysis.  ...  The Babelomics suite for functional analysis identified 16 duplicates leading to a valid list of 410 IDs.  ... 
doi:10.1038/npre.2010.5266.1 fatcat:nattq5cqp5evvh4mskv257f6jm

Charting the NF-kB pathway interactome map

Paolo Tieri, Paolo Tieri, Alberto Termanini, Elena Bellavista, Stefano Salvioli, Claudio Franceschi
2010 Nature Precedings  
Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct  ...  This interactome is intended as an open network resource available for further development, refinement and analysis.  ...  The Babelomics suite for functional analysis identified 16 duplicates leading to a valid list of 410 IDs.  ... 
doi:10.1038/npre.2010.5266 fatcat:i4x6c3q4b5ektogva7l75m6t6y

Etiology of atherosclerosis informs choice of animal models and tissues for initial functional genomic studies of resveratrol

Lukasz Huminiecki, Atanas G. Atanasov, Jarosław Horbańczuk
2020 Pharmacological Research  
Because cellular responses to the treatment with resveratrol include the changes of expression patterns, functional genomics is an attractive tool to study them.  ...  For the purposes of these studies, three types of samples were most commonly profiled with microarrays: the liver, the skeletal muscle, and peripheral blood mononuclear cells.  ...  Acknowledgements The photo of rhesus macaque is by Charles J Sharp -own work, from Sharp Photography, sharpphotography.co.uk, CC BY-SA 4.0. Figs. 2 and 3 were designed using resources from Freepik.com  ... 
doi:10.1016/j.phrs.2019.104598 pmid:32067842 fatcat:dpggrsru3fhanlhhg7wnxgha3a

Functional Approaches to Study Leaf Senescence in Sunflower [chapter]

Paula Fernandez, Sebastin Moschen, Norma Paniego, Ruth A.
2012 Senescence  
This unigene collection was used to design the first custom sunflower oligonucleotide-based microarray based on Agilent technology as a main goal for functional genomics approaches, generated within the  ...  Under this assumption, new insights into molecular senescence events might be cleared up by high-resolution microarray data, for example, considering different points of leaf development (Breeze et al  ... 
doi:10.5772/34785 fatcat:d5xzuwf7cnbt7imjw4kvayhqlm

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Michelle R. Gaither, Georgios A. Gkafas, Menno de Jong, Fatih Sarigol, Francis Neat, Thomas Regnier, Daniel Moore, Darren R. Grӧcke, Neil Hall, Xuan Liu, John Kenny, Anita Lucaci (+3 others)
2018 Nature Ecology & Evolution  
Here, we provide an annotated genome assembly for the deepsea fish Coryphaenoides rupestris and re-sequencing data to show that differentiation at non-synonymous sites in functional loci distinguishes  ...  2018) 'Genomics of habitat choice and adaptive evolution in a deep-sea sh.', Nature ecology and evolution., 2 (4). pp. 680-687.  ...  When environmental change exposes new habitats and niche potential, adaptive radiations may rapidly generate a new lineage of species 18, 19 .  ... 
doi:10.1038/s41559-018-0482-x pmid:29507380 fatcat:zm26wx44wrg5zgnjzwnmb6pveq

Metabolomics: A Way Forward for Crop Improvement

Ali Razzaq, Bushra Sadia, Ali Raza, Muhammad Khalid Hameed, Fozia Saleem
2019 Metabolites  
Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants.  ...  This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement.  ...  Our apology for not citing all the relevant work due to space limitations. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo9120303 pmid:31847393 fatcat:6md7ljmpvjakjf7oa7mcdeauoa

Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways

Mahdi Jalili, Ali Salehzadeh-Yazdi, Saeed Mohammadi, Marjan Yaghmaie, Ardeshir Ghavamzadeh, Kamran Alimoghaddam
2017 International Journal of Hematology-Oncology and Stem Cell Research  
Conclusion: The results of this meta-analysis could be useful for developing more effective therapy strategies and new targets for diagnosis and drugs.  ...  Materials and Methods: In this study, we performed a meta-analysis of gene expression profiles derived from microarray experiments and explored the background of disease by functional and pathway analysis  ...  Functional and Gene Set Analysis Functional enrichment analysis is usually performed for the interpretation of genome-scale data via biologically relevant enriched labels in a gene list and comparisons  ... 
pmid:28286608 pmcid:PMC5338275 fatcat:k6v32rdc35e25fubauh6aql6si

Modeling Human Endometrial Decidualization from the Interaction between Proteome and Secretome

Tamara Garrido-Gomez, Francisco Dominguez, Juan Antonio Lopez, Emilio Camafeita, Alicia Quiñonero, Jose Antonio Martinez-Conejero, Antonio Pellicer, Ana Conesa, Carlos Simón
2011 Journal of Clinical Endocrinology and Metabolism  
We confirm previous knowledge, describe new molecules, and we have built up a model for human in vitro decidualization as invaluable tool for the diagnosis, therapy, and interpretation of biological phenomena  ...  These data were combined with published genomic information and integrated to model the human decidualization interactome. Design: Prospective experimental case-control study.  ...  Acknowledgments The participation of T.G.-G. was supported by a grant of Ministry of Education and Science AP2007-04066 (FPU).  ... 
doi:10.1210/jc.2010-1825 pmid:21190976 fatcat:joprhfuc5zbxpiwnce4sfv2zgi

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

Erik Roger Mohlhenrich, Rachel Lockridge Mueller
2016 Evolution  
Taken together, these results further underscore the importance of studying large genomes and indicate that salamanders provide an important model system for the study of how non-drift processes (i.e.  ...  GENETIC DRIFT AND MUTATIONAL HAZARD IN THE EVOLUTION OF SALAMANDER GENOMIC GIGANTISM Salamanders have the largest nuclear genome sizes among tetrapods and, with the exception of lungfishes, among vertebrates  ...  essential genomic function (e.g. disruption of sites required for intron splicing) or a deleterious gain-of-function mutation (e.g. a premature start codon in a 5' UTR) (Lynch 2002; Lynch 2007; Lynch  ... 
doi:10.1111/evo.13084 pmid:27714793 fatcat:x7tide6gmveibfjh3qgbqnqeyi
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